The aim of this tutorial is to introduce the users to running a metadynamics calculation using plumed. We will set up
The aim of this tutorial is to introduce the users to running a metadynamics calculation using plumed. We will set up
a simple calculation on alanine dipeptide in vacuum, analize the output, and calculate free energies
a simple calculation on alanine dipeptide in vacuum, analize the output, and calculate free energies
from the simulation. We will also learn how to spot issues related to a bad choice of collective variables
from the simulation. We will also learn how to run a well-tempered metadynamics simulation and
and how to run a well-tempered metadynamics simulation.
detect issues related to a bad choice of collective variables.
\section belfast-6-lo Learning Outcomes
\section belfast-6-lo Learning Outcomes
...
@@ -16,19 +16,19 @@ Once this tutorial is completed students will:
...
@@ -16,19 +16,19 @@ Once this tutorial is completed students will:
- Know how to analyse the output of the simulation
- Know how to analyse the output of the simulation
- Know how to restart a metadynamics calculation
- Know how to restart a metadynamics calculation
- Know how to calculate free energies from a metadynamics calculation
- Know how to calculate free energies from a metadynamics calculation
- Know how to run a well-tempered metadynamics calculation using plumed
- Know how to detect issues with the choice of the collective variables
- Know how to detect issues with the choice of the collective variables
- Know how to run a well-tempered metadynamics calculation using plumed
\section Resources
\section Resources
The <a href="https://dl.dropboxusercontent.com/u/23916760/belfast-6.tar.gz" download="belfast-6.tar.gz"> tarball </a> for this project contains the following directories:
The <a href="https://dl.dropboxusercontent.com/u/23916760/belfast-6.tar.gz" download="belfast-6.tar.gz"> tarball </a> for this project contains the following directories:
- TOPO: it contains the gromacs topology and configuration files to simulate the alanine dipeptide in vacuum
- TOPO: it contains the gromacs topology and configuration files to simulate the alanine dipeptide in vacuum
- Exercise_1_2: plumed.dat is the input file to run a metadynamics simulation with 2 CVs
- Exercise_1_2: run a metadynamics simulation with 2 CVs, dihedral phi and psi
- Exercise_3: plumed.dat is the input file to restart a metadynamics simulation
- Exercise_3: restart a metadynamics simulation
- Exercise_4: analize_FES.sh is a bash script to calculate the free-energy difference between two basins as a function of simulation time
- Exercise_4: calculate freeenergies from a metadynamics simulation and monitor the convergence
- Exercise_5: plumed.dat is the input file to run a metadynamics simulation with 1 CV
- Exercise_5: run a well-tempered metadynamics simulation with 2 CVs, dihedral phi and psi
- Exercise_6: plumed.dat is the input file to run a well-tempered metadynamics simulation with 2 CVs
- Exercise_6: run a well-tempered metadynamics simulation with 1 CV, dihedral psi
